Marie Plazanet

Coupling of protein and hydration-water dynamics in biological membranes

The dynamical coupling between proteins and their hydration water is important for the understanding of macromolecular function in a cellular context. In the case of membrane proteins, the environment is heterogeneous, composed of lipids and hydration water, and the dynamical coupling might be more complex than in the case of the extensively studied soluble proteins. Here, we examine the dynamical coupling between a biological membrane, the purple membrane (PM), and its hydration water by a combination of elastic incoherent neutron scattering, specific deuteration, and molecular dynamics simulations. Examining completely deuterated PM, hydrated in H2O, allowed the direct experimental exploration of water dynamics. The study of natural abundance PM in D2O focused on membrane dynamics. The temperature-dependence of atomic mean-square displacements shows inflections at 120 K and 260 K for the membrane and at 200 K and 260 K for the hydration water. Because transition temperatures are different for PM and hydration water, we conclude that ps–ns hydration water dynamics are not directly coupled to membrane motions on the same time scale at temperatures <260 K. Molecular-dynamics simulations of hydrated PM in the temperature range from 100 to 296 K revealed an onset of hydration-water translational diffusion at ≈200 K, but no transition in the PM at the same temperature. Our results suggest that, in contrast to soluble proteins, the dynamics of the membrane protein is not controlled by that of hydration water at temperatures <260 K. Lipid dynamics may have a stronger impact on membrane protein dynamics than hydration water.

The vibrational spectrum of crystalline benzoic acid: Inelastic neutron scattering and density functional theory calculations

Vibrational spectra of several isotopomers of benzoic acid (BA) crystals have been recorded by inelastic neutron scattering and are compared with spectra calculated for different potential energy surfaces (PES). These PES were obtained within the harmonic approximation from quantum chemical density functional theory (DFT) calculations made for the monomer, the isolated dimer, and the crystal using different codes and different levels of basis functions. Without refinement of the force constants, agreement between calculated and observed spectra is already sufficient for an unambiguous assignment of all vibrational modes. The best agreement was obtained with periodic DFT calculations. The most prominent discrepancy between calculated and observed frequencies was found for the out-of-plane O–H bending modes. For these modes (as well as for the in-plane bending and the O–H stretching modes) the anharmonicity of the potential was calculated, and the anharmonic correction was shown to account for about one-thi...

Lattice Dynamics To Trigger Low Temperature Oxygen Mobility in Solid Oxide Ion Conductors

SrFeO(2.5) and SrCoO(2.5) are able to intercalate oxygen in a reversible topotactic redox reaction already at room temperature to form the cubic perovskites Sr(Fe,Co)O(3), while CaFeO(2.5) can only be oxidized under extreme conditions. To explain this significant difference in low temperature oxygen mobility, we investigated the homologous SrFeO(2.5) and CaFeO(2.5) by temperature dependent oxygen isotope exchange as well as by inelastic neutron scattering (INS) studies, combined with ab initio (DFT) molecular dynamical calculations. From (18)O/(16)O isotope exchange experiments we proved free oxygen mobility to be realized in SrFeO(x) already below 600 K. We have also evidence that low temperature oxygen mobility relies on the existence of specific, low energy lattice modes, which trigger and amplify oxygen mobility in solids. We interpret the INS data together with the DFT-based molecular dynamical simulation results on SrFeO(2.5) and CaFeO(2.5) in terms of an enhanced, phonon-assisted, low temperature oxygen diffusion for SrFeO(3-x) as a result of the strongly reduced Fe-O-Fe bond strength of the apical oxygen atoms in the FeO(6) octahedra along the stacking axis. This dynamically triggered phenomenon leads to an easy migration of the oxide ions into the open vacancy channels and vice versa. The decisive impact of lattice dynamics, giving rise to structural instabilities in oxygen deficient perovskites, especially with brownmillerite-type structure, is demonstrated, opening new concepts for the design and tailoring of low temperature oxygen ion conductors.

The structure and dynamics of crystalline durene by neutron scattering and numerical modelling using density functional methods

Abstract Inelastic neutron scattering (INS) and single crystal diffraction measurements of tetramethylbenzene (durene) are reported along with first-principles calculations, based on density functional theory (DFT), of structure and dynamics. Atomic positions obtained from refinement of the neutron scattering data and from three different DFT methodologies are in excellent agreement. Normal modes and INS spectra are calculated within the harmonic approximation using the direct cell finite displacement technique. DFT affords a reliable description of intramolecular and intermolecular interactions with the result that the vibrational spectra are well reproduced by all calculations. The advantage over traditional ab initio, single molecule calculations is the improved description of the low frequency vibrations that are influenced by intermolecular interactions. No refinement of force constants has been undertaken. This structural and vibrational analysis is discussed in the context of optical work in durene host lattices.

Structure and vibrational dynamics of the strongly hydrogen-bonded model peptide: N-methyl acetamide

Density functional theory-based methods have been used to calculate the vibrations, in the harmonic approximation, of n-methyl acetamide in the solid state. Good agreement is obtained with previously published inelastic neutron scattering spectra. The starting point for the calculation is the crystal structure, which has to be measured at the same temperature as the vibrational spectra. Unit cell and atomic coordinates have been obtained using powder neutron diffraction on the methyl-deuterated material at 2 K. The controversial assignment of the N–H stretch mode at ∼1600 cm−1, made in the original analysis of the vibrational spectra, is not supported by the calculations presented here. Neither is evidence found for the proposed double-well potential for the proton in the hydrogen bond.

Modelling molecular vibrations in extended hydrogen-bonded networks - crystalline bases of RNA and DNA and the nucleosides

Crystalline bases of RNA and DNA and nucleosides provide a topical set of compounds showing extended hydrogen bond networks in up to three dimensions. In order to understand the structure and dynamics, such as molecular vibrations, in these systems, accurate potential energy calculations based on solid state molecular models are required. First-principles calculations based on density functional theory (DFT), which employ periodic boundary conditions have been shown in recent work on van der Waals solids and solids including hydrogen-bonded dimers and one-dimensional hydrogen-bonded chains to be most appropriate. Periodic calculations allow small molecular models based on the crystalline unit cell, which naturally include all features of any hydrogen bond network, to be constructed. Periodic DFT calculations of structure and molecular vibrations of the bases and nucleosides in the solid state, based on published crystallographic data, have been performed. The vibrational spectra are compared with recently published inelastic neutron scattering (INS) measurements and the analysis of this data based on single-molecule first-principles calculations. Solid state calculations are shown to be significantly better, offering a reliable description of vibrational modes of atoms involved in hydrogen bonds, without any refinement of calculated force constants.

Communication: Crystallite nucleation in supercooled glycerol near the glass transition

Heterogeneity and solid-like structures found near the glass transition provide a key to a better understanding of supercooled liquids and of the glass transition. However, the formation of solid-like structures and its effect on spatial heterogeneity in supercooled liquids is neither well documented nor well understood. In this work, we reveal the crystalline nature of the solid-like structures in supercooled glycerol by means of neutron scattering. The results indicate that inhomogeneous nucleation happens at temperatures near T(g). Nevertheless, the thermal history of the sample is essential for crystallization. This implies such structures in supercooled liquids strongly depend on thermal history. Our work suggests that different thermal histories may lead to different structures and therefore to different length and time scales of heterogeneity near the glass transition.

Clay Swelling: New Insights from Neutron-Based Techniques

Clayey materials are complex hierarchical and deformable porous media whose structure and organization vary at different spatial scales depending on external conditions, in particular water activity. It is therefore important, on the one hand, to follow all the structural changes that are associated with the adsorption of water molecules in the interlamellar spaces (at the scale of the particles) and, on the other hand, to describe the textural modifications induced at larger scales as a result of the swelling of individual particles. Neutron-based techniques are important to achieving this multiscale description, thanks to some special features of neutrons [e.g., specific interaction with hydrogen atoms, with in addition differential interaction with isotopes (H and D), and high penetration length of neutron beams, which allows easy preparation of versatile sample-cells container]. Finally, water dynamics in the interlayers can be investigated because of the unique interaction of neutrons with hydrogen.

Crystallization on heating and complex phase behavior of α-cyclodextrin solutions

Solutions composed of α-cyclodextrin (α-CD), water, and various methylpyridines, in particular, 4-methylpyridine (4MP), undergo reversible liquid-solid transitions upon heating, the crystalline solid phases undergoing further phase transformations at higher temperatures. This unusual behavior has been characterized by an ensemble of measurements, including solubility, differential scanning calorimetry, quasielastic neutron scattering, as well as x-ray powder diffraction. For the α-CD/4MP system five crystalline phases have been identified. The unit cell parameters and corresponding changes with temperature indicate a scenario for the crystallization process. A simple model is proposed that mimics the observed disorder-order transition.

Methyl group rotational tunneling in vibrational spectra of crystals at low temperatures

Abstract The effect of methyl group nuclear spin conversion on the Raman spectra is reported for two crystals: 2,6-dibromomesitylene and 4-methylpyridine (4MP). In both crystals the tunneling splitting is large and population changes of the tunneling sublevels upon cooling to 4.2 K are easily observable as changes of intensity and lineshape in the Raman spectra of the CH3 torsional modes and of modes coupled to these. The spin conversion time at 4.2 K is 350±30 min for DBM and 170±20 min for 4MP. The intensity ratio of the lowest frequency Raman transitions of the two spin isomers is determined.